The biological implications of this work are further strengthened by the observation that chemical feature selection based on functional pathway activity leads to more predictive toxicity models (sensitivity 78.1%, specificity 87.1%).
The biased distributions of indels on different functional pathways (Table 3) further demonstrate the selective forces on them, and suggest the association between increased indels and functional adaptation.
The differential gene expression network analysis suggests that the EMD trait is the result of different emphases on these functional pathways in the high and low muscling groups.
These genome-scale comparisons make it possible to not only improve phylogeny inference but to have better accuracy on inferring functional pathways.
Furthermore, no genome-wide assessments have been undertaken to identify altered DNA methylation patterns in the context of metastasis and their effects on specific functional pathways or gene networks.
Finding that these different types of analyses converge on the same functional pathways, but typically pinpoint different sets of genes, further highlights the importance of these key genetic pathways in adaptation to the CF lung.
Much of our knowledge on the molecular functional pathways of human leukaemia is derived from experiments with cell lines rather than from work on clinical samples (Sandberg & Ernberg, 2005).
As shown on Figure 4A, functional pathways implicated in cell growth and proliferation, cell cycle, cell death, cell signaling, DNA replication, recombination and repair and protein synthesis displayed significant altered expression in both directions.
To obtain a global picture of the potential impact of RRA loci on biological processes and functional pathways, we selected all the genes in the human genome that contains at least one functionally relevant RRA loci (602 genes with at least one splicing, missense, nonsense or frameshift variant) and we searched for enriched gene sets.
Although such individual sensitivity analyses give a quantitative measure of a component's control on a functional pathway, they cannot reveal the simultaneous impacts on other parts of the system and the overall system.
